Stanford has received a vast sum of money to study a tiny population of deadly cancer cells, a gift that could help combat the heartbreak of phoenixlike disease recurrence.

The $90 million from the New York City-based Ludwig Fund will boost research at the Ludwig Center for Cancer Stem Cell Research and Medicine at Stanford’s School of Medicine, where scientists are studying cancer stem cells for ways to tear out the roots of tumors.

Stanford is one of six institutions to share in Ludwig’s $540 million contribution to the field of cancer research, announced Monday. Endowed by the late billionaire Daniel K. Ludwig, a self-made American shipping and real estate magnate who died in 1992, the fund supports cancer research that might be otherwise dependent on the whims of government or corporate support.

“This extraordinary gift will spur innovation well into the future,” said Stanford president John Hennessy, calling it “a tremendous vote of confidence.”

Billions of dollars have been spent on cancer research since President Richard M. Nixon declared war on the disease in 1971. Yet the fight is going slower than most had hoped, with small changes in the death rate over the decades since.

Part of the problem, scientists think, it that some cancers are driven by hidden cancer stem cells — which remain tenacious even after treatment, reasserting themselves and continuing to grow. Their discovery by Canadian scientist John Dick in 1994 profoundly altered our concept of cancer biology.

If such cells are proven to be the determinant of relapse, the implication for cancer therapy is enormous. Any treatment that leaves behind residual cancer stem cells would inevitably lead to a relapse.

“These are the subset of cells that self-renew — they’re the dangerous one,” said Dr. Irving Weissman, who directs Stanford’s Ludwig Center, the only cancer stem cell center of its kind.

Weissman and Dr. Michael Clarke have isolated these cells in many different types of cancers and identified ways they might be vulnerable.

They are hoping to target them through immunotherapy, which enlists key immune system cells to grind up the malignant cells and patrol against their re-emergence.

With Ludwig support, Weissman is also pressing forward with clinical trials for a therapy that could dramatically improve survival rates for women with metastatic breast cancer. In one trial, 33 percent of the women were still alive and well, compared to 7 percent of women under the standard treatment. The trial was discontinued by the sponsoring company, but with Ludwig support, Weissman and colleagues have obtained the rights to the process and plan a larger clinical trial this year.

With its latest gift, Ludwig has committed $150 million in unfettered funding to Stanford. It complements Stanford’s Cancer Initiative, a $250 million campaign to advance research and improve patient care.

“This new infusion of money will enable us to move forward into a second and third round of research in clinical trials” that will begin at Stanford and England’s University of Oxford, Weissman said.

In 1974, with no inkling that cancer stem cells even existed, Ludwig said: “I am persuaded that eventual mastery of cancer will come only from intense and unremitting scientific exploration over many decades … This should not be hindered by the changing policies of governments and the vagaries of public interest.”